Transcriptional analysis of rice tiller buds at nitrogen sensitive stage

Objectives Nitrogen affects the development of tiller buds, thus influencing the architecture and yield of rice. This study explores gene expression of rice tiller buds at the sensitive stage of N supply to reveal the possible pathways of N regulation.

Methods The rice variety, ‘Nipponbare’, was used as the experimental material and seeds were placed in a culture medium a week after germination. We used a solution containing N 2.5 mmol/L to cultivate the plants until the 3^rd leaf became fully developed. The seedlings were divided into two groups and subjected to solutions containing N 0 and 2.5 mmol/L, respectively until the 5^th leaf became fully developed. The growth of tiller buds under different N concentrations was observed to confirm rice phenotype during the N sensitive period. Samples were taken at the junction of roots and stems, these samples were used for RNA extraction. RNA samples were collected for transcriptional analysis, including differentially expressed genes. Also, GO analysis, KEGG analysis, and protein-interaction analysis were carried out.

Results Under N deficient condition, the growth of tiller buds was inhibited, and the N content in the rice plants (P < 0.05) reduced. The results of transcription analysis showed that 842 genes were differentially expressed under different N supply conditions, with 586 genes up-regulated and 256 genes down-regulated. The GO analysis showed that most of the differentially expressed genes belonged to cell, cell part, and organelle categories. KEGG analysis of DEGs revealed that the “plant hormone signal transduction” pathway was the most enriched pathway and the “N metabolism” pathway was the second. This suggests that plant hormones and N metabolism could play essential roles in regulating the growth of rice tiller bud. The differentially expressed genes mainly relates to synthesis and metabolism pathways of auxin, cytokinin, abscisic acid, salicylic acid, jasmonic acid, and nitrate reductase involved in N metabolism. Protein-interaction analysis showed that nitrate reductase possibly interacted with phytohormone.

Conclusions The transcriptome analysis of the tiller buds indicated N deficiency influenced the phytohormone biosynthesis and transduction and N metabolism at the sensitive stage. Nitrogen deficit up-regulated the expression of nitrate reductase and phytohormone genes, while down-regulated cytokinin and auxin lead to tiller bud outgrowth as a result.